Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds
ABSTRACT: Fertility is an economically important trait in livestock. Poor fertility in dairy cattle can be due to loss-of-function variants affecting any essential gene that causes early embryonic mortality in homozygotes. To identify fertility-associated quantitative trait loci, we performed single...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-02-01
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| Series: | Journal of Dairy Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0022030221010560 |
| _version_ | 1818114123835113472 |
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| author | Md Mesbah-Uddin Bernt Guldbrandtsen Aurélien Capitan Mogens Sandø Lund Didier Boichard Goutam Sahana |
| author_facet | Md Mesbah-Uddin Bernt Guldbrandtsen Aurélien Capitan Mogens Sandø Lund Didier Boichard Goutam Sahana |
| author_sort | Md Mesbah-Uddin |
| collection | DOAJ |
| description | ABSTRACT: Fertility is an economically important trait in livestock. Poor fertility in dairy cattle can be due to loss-of-function variants affecting any essential gene that causes early embryonic mortality in homozygotes. To identify fertility-associated quantitative trait loci, we performed single-marker association analyses for 8 fertility traits in Holstein, Jersey, and Nordic Red Dairy cattle using imputed whole-genome sequence variants including SNPs, indels, and large deletion. We then performed stepwise selection of independent markers from GWAS loci using conditional and joint association analyses. From single-marker analyses for fertility traits, we reported genome-wide significant associations of 30,384 SNPs, 178 indels, and 3 deletions in Holstein; 23,481 SNPs, 189 indels, and 13 deletions in Nordic Red; and 17 SNPs in Jersey cattle. Conditional and joint association analyses identified 37 and 23 independent associations in Holstein and Nordic Red Dairy cattle, respectively. Fertility-associated GWAS loci were enriched for developmental and cellular processes (Gene Ontology enrichment, false discovery rate < 0.05). For these quantitative trait loci regions (top marker and 500 kb of surrounding regions), we proposed several candidate genes with functional annotations corresponding to embryonic lethality and various fertility-related phenotypes in mouse and cattle. The inclusion of these top markers in future releases of the custom SNP chip used for genomic evaluations will enable their validation in independent populations and improve the accuracy of genomic predictions. |
| first_indexed | 2024-12-11T03:45:44Z |
| format | Article |
| id | doaj.art-ac5acc2475af4f738e89d8222d2b9adc |
| institution | Directory Open Access Journal |
| issn | 0022-0302 |
| language | English |
| last_indexed | 2024-12-11T03:45:44Z |
| publishDate | 2022-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dairy Science |
| spelling | doaj.art-ac5acc2475af4f738e89d8222d2b9adc2022-12-22T01:22:03ZengElsevierJournal of Dairy Science0022-03022022-02-01105212981313Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breedsMd Mesbah-Uddin0Bernt Guldbrandtsen1Aurélien Capitan2Mogens Sandø Lund3Didier Boichard4Goutam Sahana5Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark; Génétique Animale et Biologie Intégrative (GABI), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, FranceCenter for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, DenmarkGénétique Animale et Biologie Intégrative (GABI), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; Allice, 75595 Paris, FranceCenter for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, DenmarkGénétique Animale et Biologie Intégrative (GABI), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, FranceCenter for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark; Corresponding authorABSTRACT: Fertility is an economically important trait in livestock. Poor fertility in dairy cattle can be due to loss-of-function variants affecting any essential gene that causes early embryonic mortality in homozygotes. To identify fertility-associated quantitative trait loci, we performed single-marker association analyses for 8 fertility traits in Holstein, Jersey, and Nordic Red Dairy cattle using imputed whole-genome sequence variants including SNPs, indels, and large deletion. We then performed stepwise selection of independent markers from GWAS loci using conditional and joint association analyses. From single-marker analyses for fertility traits, we reported genome-wide significant associations of 30,384 SNPs, 178 indels, and 3 deletions in Holstein; 23,481 SNPs, 189 indels, and 13 deletions in Nordic Red; and 17 SNPs in Jersey cattle. Conditional and joint association analyses identified 37 and 23 independent associations in Holstein and Nordic Red Dairy cattle, respectively. Fertility-associated GWAS loci were enriched for developmental and cellular processes (Gene Ontology enrichment, false discovery rate < 0.05). For these quantitative trait loci regions (top marker and 500 kb of surrounding regions), we proposed several candidate genes with functional annotations corresponding to embryonic lethality and various fertility-related phenotypes in mouse and cattle. The inclusion of these top markers in future releases of the custom SNP chip used for genomic evaluations will enable their validation in independent populations and improve the accuracy of genomic predictions.http://www.sciencedirect.com/science/article/pii/S0022030221010560genome-wide association studyfertilitydeletiondairy cattle |
| spellingShingle | Md Mesbah-Uddin Bernt Guldbrandtsen Aurélien Capitan Mogens Sandø Lund Didier Boichard Goutam Sahana Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds Journal of Dairy Science genome-wide association study fertility deletion dairy cattle |
| title | Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds |
| title_full | Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds |
| title_fullStr | Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds |
| title_full_unstemmed | Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds |
| title_short | Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds |
| title_sort | genome wide association study with imputed whole genome sequence variants including large deletions for female fertility in 3 nordic dairy cattle breeds |
| topic | genome-wide association study fertility deletion dairy cattle |
| url | http://www.sciencedirect.com/science/article/pii/S0022030221010560 |
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